Data & Analytics

holobiomicslab Skill

Use when you have NMR metabolite measurements from peripheral blood samples (plasma/serum) paired with processing delay metadata (pre-centrifugation and post-centrifugation times) and need to benchmark metabolic parameter stability across delay windows.

holobiomicslab Skill

Use when after constructing MetaboSet objects from Excel-formatted LC-MS peak tables and before drift correction or quality flagging.

holobiomicslab Skill

Use when when you have read LC-MS peak table data from Excel (or equivalent) into R and need to organize it into a structured object that tracks feature abundances, sample information (injection order, QC status), and feature metadata (mass, retention time, Feature_ID) simultaneously.

holobiomicslab Skill

Use when when constructing a sample list from an Excel template for LC/GC-MS analysis, you must classify each QC sample by type before proceeding to plate layout and randomization steps.

holobiomicslab Skill

Use when when processing MS spectral data from multiple open mass spectra libraries (OMSLs) in mixed formats (MSP, MGF, JSON, CSV), especially when source data exhibits missing fields, malformed entries, inconsistent adduct representations, or non-standard format variants that may cause silent.

holobiomicslab Skill

Use when you have NMR-based metabolomics measurements from a cohort containing both plasma and serum samples with associated processing delay metadata (pre- and post-centrifugation times), and you need to determine whether metabolic parameter stability differs between the two sample types or to.

holobiomicslab Skill

Use when you have raw or semi-curated mass spectrometry spectral data in JSON, CSV, MSP, or MGF format from multiple open mass spectra libraries (OMSLs) and need to standardize field names, validate chemical identifiers (SMILES, InChI, InChIKey), remove duplicates, filter by quality criteria.

holobiomicslab Skill

Use when you have raw NMR metabolomics measurements paired with pre-analytical metadata (e.g., processing delay times, sample type designations [plasma vs. serum], cohort identifiers) and need to investigate how delays affect measured metabolic parameters.

holobiomicslab Skill

Use when when ingesting spectra from multiple open mass spectrometry libraries (OMSLs) in .mgf, .msp, .json, or .csv format and you observe mixed experimental protocols, inconsistent adduct annotations, or partial metadata.

holobiomicslab Skill

Use when when processing a multi-sample LC-MS metabolomics project after mass-track extraction and retention-time calibration have been applied to all individual samples, and you need to detect peaks across the entire cohort.

holobiomicslab Skill

Use when you have a user-supplied metabolite set file (CSV or JSON) defining custom groupings of metabolites (e.

holobiomicslab Skill

Use when when you have paired NMR metabolite measurements and corresponding processing metadata (pre-centrifugation delay, post-centrifugation delay, sample type, cohort) for a blood sample cohort and need to determine which metabolites remain stable across the expected or observed delay range, or.

holobiomicslab Skill

Use when after mass track extraction from individual LC-MS samples, when you need to align mass tracks across a cohort to produce a unified feature matrix. Specifically: when study size is ≤10 samples, use pairwise anchor-prioritized alignment;

holobiomicslab Skill

Use when when beginning an untargeted LC-MS metabolomics study and need to assemble a cohort of mzML files for processing; particularly when establishing performance baselines across sample counts (10, 50, 100+ samples), validating reproducibility, or preparing data for publication.

holobiomicslab Skill

Use when when you have a retention-time dataset (e.g., SMRT or Eawag_XBridgeC18_364) in .xlsx format and need to train or adapt a graph neural network model to predict chromatographic retention times for new compounds.

holobiomicslab Skill

Use when you have generated or curated a lipid spectral library (with precursor m/z, adduct information, charge states, retention times, and fragmentation patterns) and need to export it for use in either Excalibur-based DDA experiments on an Orbitrap mass spectrometer, or in Skyline for targeted.

holobiomicslab Skill

Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measurements for a cohort of plasma or serum samples, and you need to assess how processing delays affect metabolite concentrations and.

holobiomicslab Skill

Use when you have multiple feature tables (CSV files) from different LC-MS analytical experiments, each containing mass, retention time, intensity, isotope, and adduct annotations, and you need to merge them into a single aligned feature matrix.

holobiomicslab Skill

Use when when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation times), and paired NMR metabolomic measurements for a plasma or serum cohort, and you need to determine how processing delays impact metabolite.

holobiomicslab Skill

Use when when processing multiple LC-MS samples in a cohort study and MassGrid construction reveals that anchor mass tracks (13C/12C isotope or Na/H adduct pairs) in non-reference samples deviate systematically from the reference sample's m/z values by >1 ppm.

holobiomicslab Skill

Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) in TSV or CSV format with separate 2D and 3D structure-organism pair tables, and need to produce authoritative headline counts of unique referenced pairs, unique curated structures, unique organisms, and source.

diegosouzapw Bundle

LibreOffice Calc workflow skill. Use this skill when the user needs Spreadsheet creation, format conversion (ODS/XLSX/CSV), formulas, data automation with LibreOffice Calc and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Analytics Tracking & Measurement Strategy workflow skill. Use this skill when the user needs Design, audit, and improve analytics tracking systems that produce reliable, decision-ready data and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

holobiomicslab Skill

Use when you have a preprocessed LC-MS peak table exported from peak-picking software (e.g., MS-DIAL) in Excel format with three logical compartments: sample annotation (rows), feature annotation (columns), and abundance matrix (numeric values).

holobiomicslab Skill

Use when you have NMR metabolomics measurements paired with pre-analytical metadata (processing delay times, centrifugation timing, sample type such as plasma vs. serum, cohort identifiers) and need to interactively explore how variation in processing conditions drives changes in metabolic.

holobiomicslab Skill

Use when when you have NMR metabolite measurements paired with documented pre-centrifugation and post-centrifugation delay times, and need to assess how processing delays affect metabolic parameter stability within a plasma or serum sample cohort.

holobiomicslab Skill

Use when you have a filtered peak list (CSV with m/z values and assigned molecular formulas) from FT-ICR MS and want to infer biochemical transformations occurring in microbial or environmental samples.

holobiomicslab Skill

Use when when you have extracted mass tracks (EICs) from individual LC-MS samples and need to establish reliable landmarks for subsequent pairwise or global alignment across a cohort.

holobiomicslab Skill

Use when after individual mass tracks (EICs) have been extracted from each sample's mzML file and you need to create a unified, cross-sample m/z reference structure. Triggered when: (1) you have ≥2 samples in a cohort; (2) mass tracks have been binned at 0.

holobiomicslab Skill

Use when you have TSV or CSV files containing structure-organism pairs (with columns for structure identifier and organism identifier) and need to count unique pairs, unique structures, unique organisms, or enumerate source database identifiers to validate or report dataset scale.

holobiomicslab Skill

Use when when a user has prepared a custom collection of metabolite sets (e.g., from spectral fragmentation clustering, literature curation, or domain-specific grouping) in CSV or JSON format and wants to score their activity levels using PALS without modifying the core PALS codebase.

holobiomicslab Skill

Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation timestamps or duration), and paired NMR metabolomic measurements for a sample cohort, and you need to quantify how delays at different time-points affect.

holobiomicslab Skill

Use when you have executed a binary classifier (such as BitterPredict.m) on a set of molecules with chemical structure descriptors and need to translate the raw predictions into a structured CSV output file that maps molecule identifiers to their predicted class labels (bitter or not-bitter).

holobiomicslab Skill

Use when you have raw metabolomics data in mzML or mzXML format and need to convert it into a normalized feature table (CSV or mzTab) via automated batch processing.

holobiomicslab Skill

Use when when processing LC-MS metabolomics datasets with 10 or fewer samples and requiring reproducible mass track alignment across the cohort.

holobiomicslab Skill

Use when when testing associations between metabolic features (from NMR or MS) and a phenotype of interest (e.g., BMI, disease status) in a cohort where age, gender, or clinical confounders are known to correlate with both the metabolite and phenotype.